The ability of optical inspection tools to provide high-value results may be a strong function of their ability to filter the inspection layer of interest from underlying prior level patterns that are not of interest. In post-lithography inspections, using techniques such as process window qualifications (PWQ), wafers may be inspected at the lithography step with multiple process conditions. Test macros for routine inspections may be generally performed on flat bare silicon monitors to simulate a production process. There are difficulties in routine inspections with product wafers that contain multiple film stacks, primarily due to interference from underlying films, and underlying film topography. This is particularly an issue in the back end of line (BEOL), where lithography focus budgets erode relative to intra-die topography. There exists a need for a method for inspecting real product substrates with topography that may influence scanner focus control in very non-obvious manners, in order to accurately assess the process center.